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The PEP group; formal research projects, status July 2007

Projects related to chitin, chitosan and chito-oligosaccharides

  • NFR project 140497 “Characterization and engineering of enzymes for the conversion of chitin and related polymers”, 2001 – 2008. This is an old project where there still is 1 year of Ph.D. work left due to parental leaves along the way. This project is a collaboration with Prof. Kjell M. Vårum et al. at NTNU, the Norwegian University of Science and Technology in Trondheim. Principle worker on this project: Ph.D. student Ingunn Alne Hoell (at UMB). SUMMARY: Chitin and its (partially) deacetylated forms (chitosans) are abundant biopolymers whose degradation products (chito-oligosaccharides) have a wide variety of highly interesting potential applications. These applications include use as elicitors of plant-defence responses, anti-fungals, medicines against arthritis, and food ingredients. Further exploration of potentially high-value chito-oligosaccharides is limited by the lack of technology to convert chitin/chitosan into oligosaccharides of defined length and composition. The goal of the present project is to develop a set of enzymes (chitinases) that can be used for industrial conversion of (partially deacetylated) chitin into useful products. To achieve this goal, naturally occurring chitinases and chitin-binding proteins will be characterized in great detail, in particular with respect to substrate- and product- specificity. These studies include the use of advanced analytical methods and separation techniques in carbohydrate chemistry. Promising chitinases will be optimized by classical protein engineering and by random mutagenesis approaches (e.g. gene shuffling), followed by high-throughput screening for interesting mutants. Enzymes will be optimized in terms of their stability under relevant conditions and in terms of their ability to convert chitin or related polymers into chito-oligosaccharides of defined length and sugar composition. Optimized enzymes will be used for producing (mixtures of) chito-oligosaccharides whose biological activities will be tested.
  • NFR project 164653 “Characterization and exploration of microbial enzymes for processing of chitin, chitosan and peptidoglycan”. 1 Ph.D. + 1 post-doc + 0.5 technician, spread over 2006 – 2009 (because of parental leaves). This project is a collaboration with Prof. Kjell M. Vårum at NTNU, the Norwegian University of Science and Technology in Trondheim. Principle worker on this project: Ph.D. student Ellinor Heggset (at NTNU); Post-doc Zhanliang Liu (at UMB); engineer Anne Cath Bunæs (at UMB). SUMMARY: The availability of an increasing number of microbial genomes, including the genome of the highly versatile white-rot basidiomycete Phanerochaete chrysosporium, offers unique possibilities to study and explore enzymes with potential biotechnological applications. In the present project, we will use available microbial genomes as well as comparative genomics (on a gene-to-gene basis) to overexpress, characterize, improve and exploit two types of enzymes for processing of the important marine biopolymer chitin and its derivative chitosan. The overall long-term goal behind this project is to develop enzyme-based technologies to convert the low value (waste) material chitin (a polymer of N-acetylglucosamine) into high-value chito-oligosaccharides with biological activities. We will (1) clone and overexpress chitosanase- and deacetylase-encoding genes from microbial genomes, (2) characterize the enzymes in detail, (3) conduct structure-function studies to understand how the enzymes work as well as to tailor their performance, and, (4) use the new enzymes to convert chitin and chitosan to chito-oligosaccharides with known length, composition and sequence. The functionality of these oligosaccharides will be tested, e.g. in terms of their anti-fungal activities, enzyme inhibiting activities and immunostimulatory activities, as well as in terms of their ability to elicit defence responses in plants. The present project will also touch upon peptidoglycan modification in Gram-positive bacteria by deacetylases, which is of medical importance. By comparing genomes and the results of this project, the potential of deacetylases as a target protein for drug development will be evaluated.
  • NFR, strategic university programme, “Business-related biotechnology at UMB”. 2007 & 2008. Principle worker on this project: Post-doc researcher Berit Aam.
  • NFR project 178428 “Applying advanced computational and experimental tools to explore surface electrostatics in chitinases”. 2007 – 2010. Principle worker on this project: Post-doc researcher Sigrid Gåseidnes.
  • NFR project 171991 “Degradation of insoluble carbohydrate polymers: how do microbial chitinolytic machineries work?” Principle worker on this project: Post-doc researcher Gustav Vaaje-Kolstad.
  • UMB Ph.D. fellowship; “Use of tailor-made chitinases to synthesize oligosaccharide-based bioactive compounds”. 2006 – 2010. Ph.D. student Henrik Zakkariassen (co-supervised by Dr. Morten Sørlie)

Lactic acid bacteria projects

  • NFR strategic University project 159058 “Molecular biology of Gram-positive bacteria: functional genomics and applications”, 2004-2008. This large project has a total NFR allocation of 23 million and is a collaboration between various groups at our institute and Matforsk, The Norwegian Food Research Institute. The project leader is Prof. Ingolf F. Nes. The PEP group has one post-doc researcher, Dr. Geir Mathiesen.
  • UMB special “SFF” Ph.D. fellowship “Protein production and secretion in lactobacilli”. 2007 – 2011. Ph.D. student Lasse Fredriksen.
  • UMB, Ph.D. fellowship “Functional genomics of Enterococcus faecalis – a proteome approach”. 2006 – 2010. This is a collaboration with the group of Professor Ingolf Nes. Ph.D. student Liv Anette Bøhle.
  • NFR FUGE project 183637 “Secretomes of lactobacilli and enterococci and their impact on bacterial adaptation and human health”. 2008 – 2010; two open positions.

Biomass, biofuels, bioprospecting and applied enzymology

  • NFR project 167863/I10, ”ADDBAR: Added value products from barley” (2005 – 2009). This is a collaboration with Matforsk, The Norwegian Food Research Institute. The project leader is Dr. Svein H. Knutsen at Matforsk. Our primary activity: enzymatic modifications of barley fractions. The PEP group has about 2.5 years of post-doc funding. Principle workers: Drs. Svein J. Horn & Bjørge Westereng.
  • NFR project 178282/I10, “Conversion of salmon by-products to high-value ingredients of growth media for probiotic bacteria”. 2007-2009. 1 Post-doc. This is a collaboration with the company Marine Harvest and with SINTEF, Trondheim. Principle worker (as off October 2007): post-doc researcher Janneke Treimo.
  • EU, FP6 Strep, FOOD-CT-2005-006922; REPRO: Reducing Food Processing Waste (our primary role: enzymatic upgrading of brewer’s spent grain). 2005 – 2008. Project leader: Dr. Keith Waldron, at IFR, Norwich, UK. The PEP group has about 2 years of post-doc funding. Principle workers: post-doc researchers Janneke Treimo, Svein J. Horn & Bjørge Westereng.
  • Industry project “Enzyme technology for the production of bioethanol from woody materials”. This work is being done for a group of bioenergy consultants/investors (www.enconsult.net). Principle worker: post-doc researcher Svein J. Horn .
  • UMB-financed Ph.D. fellowship “Enzyme discovery for biomass conversion”. 2007-2011. This is a collaboration with The Norwegian Forest and Landscape Institute (on wood degrading fungi). Open Ph.D. position.